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About a formamide-based origin of informational polymers: syntheses of nucleobases and favourable thermodynamic niches for early polymers.

Formamide NH(2)CHO chemistry provides a unitary frame into which several pieces of the origin-of-life puzzle may be adjusted. Synthetic processes were uncovered which, starting from formamide and prebiotically easily available common catalysts, yield all the necessary nucleic bases precursors, including acyclonucleosides. Formamide allows phosphorylations and trans-phosphorylations, favours the micellar aggregation of surfactants and, most importantly, determines conditions in which the formation of nucleic polymers is thermodynamically favoured. In the detected conditions, the phosphoester bonds are more stable in the polymeric than in the monomeric form, thus allowing formation and survival of informational nucleic polymers.

Evolution, Chemical↗

Identification of superactive centers in thermally treated formamide-intercalated kaolinite.

The thermal behavior of a formamide-intercalated mechanochemically activated (dry-ground) kaolinite was investigated by thermogravimetry-mass spectrometry (TG-MS) and diffuse reflectance Fourier transform infrared spectroscopy (DRIFT). After the removal of adsorbed and intercalated formamide, a third type of bonded reagent was identified in the temperature range 230-350 degrees C decomposing in situ to CO and NH3. The presence of formamide decomposition products, as well as CO2 and various carbonates identified by DRIFT spectroscopy, indicates the formation of superactive centers as a result of mechanochemical activation and heat treatment (thermal deintercalation). The structural variance of surface species decreases with the increase of grinding time. The unground mineral contains a small amount of weakly acidic and basic centers. After 3 h of grinding, the number of acidic centers increases significantly, while on further grinding the superactive centers show increased basicity. With the increase of grinding time and treatment temperature the number of bicarbonate- and bidentate-type structures decreases in favor of the carboxylate- and monodentate-type ones.

Formamides↗

The role of molecular size in the excited state behavior of aminocoumarin dyes in restricted media--2: study of BC I in AOT-formamide reversed micelles.

Ground and excited state properties of a pre-twisted 7-diethylaminocoumarin dye (BC I) belonging to the family of coumarinyl benzopyrano pyridines are reported in isooctane-AOT-formamide reversed micelles. In reversed micelles, BC I, albeit soluble in formamide, is found to remain out of the polar solvent pool. But the photophysical properties of the probe dye are sensitive to the changes in the polarity of the interfacial region caused by increase in F0 = [formamide]/[AOT]. The spectroscopic properties and dynamics are indicative of dual emission due to the solubilization of the dye in two different environments (the nonpolar solvent and the interfacial region). Results of the steady-state fluorescence anisotropy experiments also support the presence of two different environments. The present study once again proves that molecular size is an important parameter in the study of the photophysical properties of the flexible aminocoumarin dyes in reversed micelles.

Coumarins↗

Preferential solvation of Brooker's merocyanine in binary solvent mixtures composed of formamides and hydroxylic solvents.

The ET polarity values of 4-[(1-methyl-4(1H)-pyridinylidene)-ethylidene]-2,5-cyclohexadien-1-one (Brooker's merocyanine) were collected in mixed-solvent systems comprising a formamide [N,N-dimethylformamide (DMF), N-methylformamide (NMF) or formamide (FA)] and a hydroxylic (water, methanol, ethanol, propan-2-ol or butan-1-ol) solvent. Binary mixtures involving DMF and the other formamides (NMF and FA) as well as NMF and FA were also studied. These data were employed in the investigation of the preferential solvation (PS) of the probe. Each solvent system was analyzed in terms of both solute-solvent and solvent-solvent interactions. These latter interactions were responsible for the synergism observed in many binary mixtures. This synergistic behaviour was observed for DMF-propan-2-ol, DMF-butan-1-ol, FA-methanol, FA-ethanol and for the mixtures of the alcohols with NMF. All data were successfully fitted to a model based on solvent-exchange equilibria, which allowed the separation of the different contributions of the solvent species in the solvation shell of the dye. The results suggest that both hydrogen bonding and solvophobic interactions contribute to the formation of the solvent complexes responsible for the observed synergistic effects in the PS of the dye.

1-Butanol↗

Vibrational spectroscopy of formamide-intercalated kaolinites.

The vibrational spectroscopy of low and high defect kaolinites fully and partially intercalated with formamide have been determined using a combination of X-ray diffraction, DRIFT and Raman spectroscopy. Expansion of the high defect kaolinite to 10.09 A resulted in a decrease in the peak width of the d(001) peak attributed to a decrease in defect structures upon intercalation. Changes in the defect structures of the low defect kaolinite were observed. Additional infrared bands were observed for the formamide intercalated kaolinites at 3629 and 3606 cm(-1). The 3629 cm(-1) band is attributed to the hydroxyl stretching frequency of the inner surface hydroxyl group hydrogen bonded to the carboxyl group of the formamide. The 3606 cm(-1) band is ascribed to water in the interlayer. Concomitant changes are observed in both the hydroxyl deformation modes and in the carboxyl bands.

Amides↗

Structure of three class I human alcohol dehydrogenases complexed with isoenzyme specific formamide inhibitors.

Formamides are aldehyde analogues that have demonstrated potent and selective inhibition of human alcohol dehydrogenase isoenzymes. The alphaalpha, beta(1)beta(1), gamma(2)gamma(2), and sigmasigma isoforms have all been found to be strongly inhibited by substituted formamides. In this paper, the structure of the alphaalpha isoform of human alcohol dehydrogenase complexed with N-cyclopentyl-N-cyclobutylformamide was determined by X-ray crystallography to 2.5 A resolution, the beta(1)beta(1) isoform of human alcohol dehydrogenase complexed with N-benzylformamide and with N-heptylformamide was determined to 1.6 and 1.65 A resolution, respectively, and the structure of the gamma(2)gamma(2) isoform complexed with N-1-methylheptylformamide was determined to 1.45 A resolution. These structures provide the first substrate-level view of the local structural differences that give rise to the individual substrate preferences shown by these highly related isoenzymes. Consistent with previous work, the carbonyl oxygen of the inhibitors interacts directly with the catalytic zinc and the hydroxyl group of Thr48 (Ser48 for gamma(2)gamma(2)) of the enzyme. The benzene ring of N-benzylformamide and the carbon chains of N-heptylformamide and N-1-methylheptylformamide interact with the sides of the hydrophobic substrate pocket whose size and shape is dictated by residue exchanges between the beta(1)beta(1) and gamma(2)gamma(2) isoenzymes. In particular, the exchange of Ser for Thr at position 48 and the exchange of Val for Leu at position 141 in the gamma(2)gamma(2) isoenzyme create an environment with stereoselectivity for the R-enantiomer of the branched N-1-methylheptylformamide inhibitor in this isoenzyme. The primary feature of the alphaalpha isoform is the Ala for Phe93 exchange that enlarges the active site near the catalytic zinc and creates the specificity for the branched N-cyclopentyl-N-cyclobutylformamide inhibitor, which shows the greatest selectivity for this unique isoenzyme of any of the formamide inhibitors.

Alcohol Dehydrogenase↗

Multiple isotope effect study of the acid-catalyzed hydrolysis of formamide.

Multiple isotope effects were measured at the reactive center of formamide during acid-catalyzed hydrolysis in water at 25 degrees C. The mechanism involves a rapid pre-equilibrium protonation of the carbonyl oxygen, followed by the formation of at least one tetrahedral intermediate, which does not appreciably exchange its carbonyl oxygen with the solvent (kh/kex = 55). The pKa for formamide was determined by 15N NMR and found to be about -2.0. The formyl-hydrogen kinetic isotope effect (KIE) is indicative of a transition state that is highly tetrahedral (Dkobs = 0.79); the carbonyl-carbon KIE (13kobs = 1.031) is in agreement with this conclusion. The small leaving-nitrogen KIE (15kobs = 1.0050) is consistent with some step prior to breaking the C-N bond as rate-determining. The carbonyl-oxygen KIE (18kobs = 0.996) points to attack of water as the rate-determining step. On the basis of these results, a mechanism is proposed in which attachment of the nucleophile to a protonated formamide molecule is rate determining.

Acids↗

Ribonucleic acid-deoxyribonucleic acid hybridization in aqueous solutions and in solutions containing formamide.

Hybridization in 6xSSC (SSC, 0.15m-sodium chloride-0.015m-sodium citrate) at 66 degrees C was compared with hybridization in formamide-6xSSC (1:1, v/v) at 35 degrees C. As expected, the RNA hybridization potential was labile in the former system and stable in the latter. DNA retention by filters was poor in the formamide system, but could be improved. Several other properties of the hybridization reaction were explored and it was concluded that the formamide system is generally superior.

Amides↗

A novel method using formamide for the elution of antibodies from erythrocytes.

BACKGROUND AND OBJECTIVES: Accurate identification of antibodies that sensitize red blood cells (RBCs) involves dissociating them from RBCs using an in vitro elution method that does not alter their antigen-binding properties, and analysis of the eluates against a panel of RBCs. MATERIALS AND METHODS: A method was developed that allowed efficient RBC antibody elution. Human polyclonal anti-D was used to sensitize Rh-positive RBCs, and known antigen-antibody disruptive reagents were tested using these RBCs. The best reagent conditions were optimized. Eluates made were tested and compared to results obtained with a glycine-acid-based commercial elution kit to determine efficacy. Patient samples that were positive with direct antiglobulin tests (DATs), and in vitro commercial antisera-sensitized RBCs representing clinically significant antibodies, were used for evaluating the new method. RESULTS: The formamide method was efficient at removing antibodies from RBCs. The patient samples with a positive DAT had antibodies recovered with the same specificity when compared to the acid-based technique. The length of preparation time was similar for both formamide and acid-based methods. Results of testing the eluates made from reagent RBCs sensitized with commercial antisera were distinct with antigen-positive and -negative erythrocytes. CONCLUSIONS: The formamide method compares well with acid techniques and may be an alternative choice of elution method.

Agglutination Tests↗

Photocatalysis and the origin of life: synthesis of nucleoside bases from formamide on TiO2(001) single surfaces.

We report the conversion of a large fraction of formamide (NH(2)CHO) to high-molecular-weight compounds attributed to nucleoside bases on the surface of a TiO(2) (001) single crystal in ultra-high vacuum conditions. If true, we present previously unreported evidence for making biologically relevant molecules from a C1 compound on any single crystal surface in high vacuum and in dry conditions. An UV light of 3.2 eV was necessary to make the reaction. This UV light excites the semiconductor surface but not directly the adsorbed formamide molecules or the reaction products. There thus is no need to use high energy in the form of photons or electrical discharge to make the carbon-carbon and carbon-nitrogen bonds necessary for life. Consequently, the reaction products may accumulate with time and may not be subject to decomposition by the excitation source. The formation of these molecules, by surface reaction of formamide, is proof that some minerals in the form of oxide semiconductors are active materials for making high-molecular-weight organic molecules that may have acted as precursors for biological compounds required for life in the universe.

Carbon↗

Structural study of DNA duplex containing an N-(2-deoxy-beta-D-erythro-pentofuranosyl) formamide frameshift by NMR and restrained molecular dynamics.

The presence of an N-(2-deoxy-beta-D-erythro-pentofuranosyl) formamide (F) residue, a ring fragmentation product of thymine, in a frameshift context in the sequence 5'-d-(AGGACCACG)*d(CGTGGFTCCT) has been studied by 1H and 31P nuclear magnetic resonance (NMR) and molecular dynamics. Two-dimensional NMR studies show that the formamide residue, whether the cis or trans isomer, is rotated out of the helix and that the bases on either side of the formamide residue in the sequence, G14 and T16, are stacked over each other in a way similar to normal B-DNA. The cis and trans isomers were observed in the ratio 3:2 in solution. Information extracted from 31P NMR data reveal a modification of the phosphodiester backbone conformation at the extrahelical site, which is also observed during the molecular dynamics simulations.

Base Sequence↗

Evaluation of the developmental toxicity of formamide in New Zealand white rabbits.

Naturally mated female New Zealand White (NZW) rabbits (24/group) received formamide (35, 70, or 140 mg/kg/day) or vehicle (1 ml/kg deionized/distilled water) by gavage on gestational days (GD) 6 through 29. The study was conducted using a 2-replicate design. Maternal food consumption (absolute and relative), body weight, and clinical signs were monitored at regular intervals throughout gestation. One and four maternal deaths occurred at the low and high doses, respectively. Abortions or early deliveries were noted in 0, 2, 2, and 8 females in the 0, 35, 70, and 140-mg/kg/day dose groups, respectively. Other clinical signs associated with formamide exposure were minimal: primarily reduced or absent fecal output at the high dose (2-13 animals/day). Also at the high dose, maternal body weight was significantly depressed on GD 21, 24, and 27 (87-90% of the control value); maternal body weight gain was significantly reduced for GD 12 to 15, 18 to 21, and 21 to 24 (treated animals gained less than 1 g, or lost up to 100 g). In addition, maternal body weight gain was reduced at the middle dose for GD 18 to 21. Maternal body weight gain, corrected for gravid uterine weight, was unaffected. Relative maternal food consumption in the high-dose group was 34-59% of control intake from GD 12 through GD 24, but was comparable to controls thereafter. At termination (GD 30), confirmed-pregnant females (9-20 per group) were evaluated for clinical status, liver weights, and gestational outcome; live fetuses were examined for external, visceral, and skeletal malformations and variations. Maternal liver weight (absolute or relative to body weight) was unaffected by treatment, but gravid uterine weight at the high dose was 71% of the control value. A significantly increasing trend was noted for the percent non-live implants per litter. In addition, although not statistically significant from the control group, the values for the percent late fetal deaths per litter and percent non-live implants per litter in the 140-mg/kg/day group were higher than maximum historical values, suggesting an increase in late gestational deaths in the surviving high-dose animals. Formamide decreased the mean number of live fetuses per litter at the high dose to 66% of the control value. Mean fetal body weight per litter for males and the sexes combined was significantly decreased at the high dose; mean female fetal body weight was also decreased, although the difference did not reach statistical significance. There was no effect of treatment on the incidence of external, visceral, or skeletal malformations or variations in animals surviving to scheduled necropsy. In summary, the no-observed-adverse-effect level (NOAEL) for maternal toxicity was 70 mg/kg/day and the lowest-observed-adverse-effect level (LOAEL) was 140 mg/kg/day under the conditions of this study. Similarly, the NOAEL for developmental toxicity was 70 mg/kg/day and the LOAEL was 140 mg/kg/day.

Animals↗

Isolation of polymerization-competent cytoplasmic actin by affinity chromatography on immobilized DNAse I using formamide as eluant.

Formamide dissociates the G-actin . DNAse-I complex and is therefore suitable as an alternative to the eluant containing 3 M guanidinium hydrochloride, suggested originally by Lazarides and Lindberg [Proc, Natl Acad. Sci. USA, 71, 4742--4746 (1974)], to elute actin from immobilized DNAse-I agarose. Formamide provides the advantage of being a much weaker denaturant than guanidinium hydrochloride and being a nonionic substance. In the concentration necessary for the dissociation of the G-actin . DNAse-I complex (approximately 10 M) formamide denatures actin only slowly (half-time approximately 150 min at 2 degrees C) and thus allows the recovery of a large fraction of actin in a polymerization-competent form from the affinity column. Based on these findings a rapid two-step procedure for the isolation of non-muscle G-actin from cultured cells is described. The actin obtained in high yield and purity (greater than 90%) and can readily polymerize to F-actin.

Actins↗

Effect of formamide on the capsid morphology of adenovirus types 4 and 7.

Treatment of adenovirus types 4 and 7 with formamide disrupted the virions, degrading the capsids into predominantly single capsomers. As shown by electron microscopic observation, disruption proceeded in the following sequence: (i) reduction of the electron density of the virions, suggesting release of an internal component; (ii) progressive cleavage of the capsid into two or more segments and the formation (type 7 only) of capsomer "sheets"; (iii) final cleavage of the capsid into single or groups of a few capsomers. The sequence appeared similar for both adenoviruses; for both types, the rate and extent of disruption were dependent on the formamide concentration, but type 7 was more easily disrupted than type 4 by short-term (5 to 10 sec) treatment at the low (10%) concentration. At 30% formamide, the intercapsomer bonds of either type were fully cleaved, and the capsids were completely degraded into predominantly single capsomers. Pretreatment with formaldehyde did not prevent this degradation. Under suitable conditions, virus-derived remnants can be observed among the breakdown products. These remnants have been shorn of capsomers and presumably represent intact internal nucleoprotein.

Adenoviridae↗

Demonstration of mRNA using digoxigenin labelled oligonucleotide probes for in situ hybridisation in formamide free conditions.

The value of formamide for use in in situ hybridisation (ISH) for the detection of mRNA, using either single or multi probe cocktails of digoxigenin labelled oligoprobes, was investigated. Three peptides with cell specific localisation in three separate tissues--calcitonin in the thyroid, epidermal growth factor (EGF) in the submaxillary gland, and insulin in the pancreas were studied. In each case localisation was confined to the appropriate cell type, but in the presence of formamide higher concentrations of probe and a longer development time were required. The abolition of formamide from the protocol for ISH makes the technique safer, cheaper, faster and more suitable for routine diagnostic use.

Animals↗

Molecular weight of an extremely hydrophobic protein, zein, in dimethylformamide and in formamide.

Both alpha zein purified from a commericial preparation and beta zein prepared fresh from corn are soluble in the nonaqueous solvents formamide and dimethylformamide; in this regard zein resembles water soluble proteins such as insulin, ribonuclease, and lysozyme. On the basis of osmotic pressure measurements made in both formamide and dimethylformamide, alpha zein has a number average moleular weight of 21000-24000 daltons and shows no tendency to aggregate or dissociate. Beta zein exists in an aggregated state (dimer and higher forms) in dimethylformamide. Formamide dissociates the beta zein dimer into monomer units but aggregation to higher species occurs with increasing protein concentration.

Binding Sites↗

Biological effects of acetamide, formamide, and their monomethyl and dimethyl derivatives.

The industrial use of certain acetamides and formamides (particularly DMAC and DMF) for their solvent properties has resulted in rather extensive examination of their biological properties. Both DMAC and DMF are rapidly absorbed through biological membranes and are metabolized by demethylation first to monomethyl derivatives and then to the parent acetamide or formamide. Relatively high single doses to various species following oral, dermal, i.p., i.v., or inhalation exposures generally are required to produce mortality. The liver is the primary target following acute high level exposure, but massive doses can also produce damage to other organs and tissues. Repeated sublethal treatment by various routes also shows the liver to be the target organ with the degree of damage being proportional to the amount absorbed. With MMF, the potential usefulness as a cancer chemotherapeutic agent needs to be measured against the hepatotoxic effects produced in man. Acetamides and formamides are generally inactive in mutagenicity tests. Mammalian test systems do not appear to be genetically sensitive and DMF has been recommended for use as the vehicle in microbial assays designed to test for genetic activity of hard-to-dissolve chemicals. Embryotoxicity can be demonstrated at high doses; doses which generally show toxicity to the maternal animals. Structural abnormalities in sensitive species such as the rabbit are produced following exposure at near-lethal levels. The spectrum of abnormalities seen is broad and fails to show any time or site specificity in terms of developing organs/organ systems. Inhalation exposures to DMAC and DMF at levels producing some maternal toxicity in rats have produced no teratogenic response and only slight evidence of embryotoxicity. Long-term feeding of relatively high levels of acetamide produces liver cancer in rats. DMAC and DMF appear to be noncarcinogenic. The environmental toxicity of these chemicals is low. Liver damage can be produced by overexposure to these chemicals in man. Airborne concentrations need to be controlled and care should be taken to avoid excessive liquid contact as the chemicals are absorbed through the skin. A relationship exists between the amount of DMAC or DMF absorbed and the amount of MMAC or MMF excreted in the urine so that biomonitoring of the urinary metabolites can indicate situations in which total exposures, both dermal and inhalation, are excessive. An interaction between DMF and ethanol occurs such that signs, including severe facial flushing, appear when DMF-exposed individuals consume alcoholic beverages.

Acetamides↗

The incomplete denaturation of DNA in N,N-dimethyl formamide.

In this paper we show that the extent of DNA denaturation achieved by dialysis against N,N-dimethyl formamide depends on both the source of DNA and the buffer used. The stability against denaturation increases with the guanine plus cytosine content. The base sequence also plays a minor role. This behavior is due to differences in the solubility of DNA in the denaturing solvent. The DNAs with a high guanine-cytosine content have a lower solubility in dimethyl formamide and this fact results in a higher stability against denaturation. As a practical consequence, in order to achieve complete denaturation of DNA by dialysis against dimethyl formamide, it is necessary to start with DNA dissolved in a buffer of low ionic strength, preferably below 10(-3) M.

Buffers↗